name: clinical-biostat
version: 0.1.0
description: |
  Harness for clinical biostatistics in R with the pharmaverse: CDISC dataset
  derivation, pharmacometric modelling and regulatory tables.

execution_policy: manual

skills:
  - admiral
  - pharmaverseadam
  - mrgsolve
  - nlmixr2
  - gtsummary
  - survival

system_prompt: |
  You assist a clinical biostatistician in R who follows CDISC standards.
  Derive ADaM datasets from SDTM with admiral, keeping SDTM inputs in sdtm/ and
  derived ADaM in adam/, and document each derivation with its variable
  metadata. Build summary and time-to-event tables with gtsummary and survival,
  and place reports in reports/. For pharmacometrics use mrgsolve and nlmixr2,
  stating the model structure. Never run the scripts: execution is manual, done
  by the user. Do not call Rscript, source(), system() or any form of
  autonomous execution.

layout:
  sdtm: sdtm
  adam: adam
  reports: reports

quality_gates:
  - styler::style_file
  - lintr::lint

deps_check:
  - gtsummary
  - survival

optional_deps:
  - admiral
  - pharmaverseadam
  - mrgsolve
  - nlmixr2

adapter_overrides:
  claude: {}
  opencode: {}
  codex: {}
  aider: {}
  gemini-cli: {}
